According to a recent Ofsted report, there is no proven relationship between the quality of the authority and attainment in its schools, the Dumfries and Galloway director said.
Referring to a school on his own patch, Mr Sanderson had seen how inspectors were confounded by a school which was performing successfully "despite its management".
"We cannot afford to have inspections throwing up examples of local authorities where the schools are doing well 'despite the education department'," he said.
HMI is now halfway through its programme of authority inspections and has criticised East Dunbartonshire and Scottish Borders, both of which are among the leaders in terms of results.
As reported in last week's TES Scotland, directors want the inspectors to take a broader view of their department's place within wider council policies and their lines of command to chief executives and councillors.
Mr Sanderson said the messages from the national debate on education were not all insipid and anodyne. "The system needs to be changed but we don't need to rush at it since it is not in crisis. However, there are major issues to be addressed in terms of the curriculum, of the assessment procedures, of the fact that there is a large section of the student community whose needs are not being met, of the need to introduce more life skills," he said.
The country had to have strong research evidence to justify its approach and that included improved school-based self-evaluations. HMI had already highlighted its finding that 40 per cent of schools are still only fair or unsatisfactory when it comes to evaluating themselves.